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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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RNA Editing02:23

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Updated: Nov 3, 2025

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
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Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing.

Bryan R Cullen1, Kevin Tsai2,3

  • 1Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.

Methods in Molecular Biology (Clifton, N.J.)
|June 4, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces a high-resolution method for mapping RNA modifications. The photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) technique improves upon traditional RNA immunoprecipitation (RIP) for precise gene regulation studies.

Keywords:
Epitranscriptomic RNA modificationRNA immunoprecipitationac4Cm5Cm6A

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Epitranscriptomic RNA modifications are crucial for gene regulation.
  • Mapping RNA modification sites is essential for understanding their biological roles.
  • Traditional RNA immunoprecipitation (RIP) is a common but limited method for mapping these sites.

Purpose of the Study:

  • To introduce and validate a high-resolution method for mapping RNA modification sites.
  • To improve upon the resolution and background noise of traditional RIP methods.
  • To demonstrate the adaptability of the method for various RNA modifications.

Main Methods:

  • Utilized photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP).
  • Combined PAR-CLIP with RNA modification-specific antibodies.
  • Adapted the photo-crosslinking-assisted m6A sequencing (PA-m6A-seq) approach.

Main Results:

  • Achieved higher resolution mapping of RNA modifications compared to traditional RIP.
  • Demonstrated significantly lower background noise in mapping results.
  • Showcased the method's versatility for different RNA modifications.

Conclusions:

  • The described PAR-CLIP method offers a superior approach for mapping RNA modifications.
  • This technique enhances the understanding of epitranscriptomic regulation.
  • The method is adaptable for any RNA modification with available antibody support.